Chimera Commands Index

pdbrun [ all ] [ conect ] [ nouser ] [ nowait ] command [cmd_args...]

Pdbrun causes command and cmd_args to be passed to the user's system shell for execution. A set of concatenated PDB files describing the current models (hereafter referred to as a PDBRUN file) is also passed as standard input to command. Normal shell metacharacters (notably output redirection) can be used. Errors are ignored and any shell output is interpreted as commands and executed. For example, on a UNIX system,

pdbrun cat > file
would create a PDBRUN file named file that describes the current models (see also the save and write commands).

The all option specifies that all atoms, not just those that are displayed, should be sent to command.

The conect [sic] option specifies that PDB-standard CONECT records should be generated for all residues, even if they have standard connectivity.

USER records are placed in the PDBRUN file to indicate display information such as atom colors, view direction, clipping planes, etc. The nouser option specifies that no USER records should appear in the file.

By default, Chimera waits for command to exit before continuing. The nowait option causes Chimera to continue without waiting for command to exit.

Any output from command is interpreted as commands and executed. Control returns to the user interface when the pdbrun command terminates. The pdbrun command facilitates additions to the normal command set. For example, the conic command is implemented using pdbrun.

As mentioned above, a PDBRUN file is passed as input to command. This file describes not only current model coordinates, but also other aspects of the modeling environment such as clipping plane positions. Modeling environment annotations are supplied in various types of USER records, described in detail in Appendix 1 of the MidasPlus User's Manual.

The PDBRUN file has three principal sections:

  1. Annotation Headers has global modeling information.
  2. Per Molecule Annotations has molecular data for each model. Each model's data starts with a USER FILE record and is terminated with an END record. The serial numbers in ATOM, HETATM, and TER records increment continuously from one model to the next. Due to field widths, this imposes a limit of 99999 atoms in a scene. Any PDB records present in the model's original source file (and not normally interpreted for display purposes, such as REMARK records) are preserved and placed just after the USER FILE record.
  3. Annotation Trailers contains records specifying the angles and distances being explicitly monitored in the current view.

Throughout, fields in PDB records that are not wide enough to hold their associated values are filled with asterisks instead. Details of the meaning and format of the USER records employed by pdbrun can be found in Appendix 1 of the MidasPlus User's Manual. However, as there are no Midas-style nonmolecular objects in the framework of the Midas emulator in Chimera, PDBRUN files created therein will not contain any USER OBJ, USER ENDOBJ, or USER GFX records.

A discussion of the motivation for and design criteria of the PDBRUN format can be found in: G. S. Couch, E. F. Pettersen, C. C. Huang and T. E. Ferrin "Annotating PDB files with scene information" J. Mol. Graphics 13, 153-158 (1995).

See also: runscript, save, system, write, export, writesel